HEREDITARY aims to significantly transform the way we approach disease detection, prepare treatment response, and explore medical knowledge by building a robust, interoperable, trustworthy and secure framework that integrates multimodal health data (including genetic data) while ensuring compliance with cross-national privacy-preserving policies. The HEREDITARY framework comprises five interconnected layers, from federated data processing and semantic data integration to visual interaction. By utilizing advanced federated analytics and learning workflows, we aim to identify new risk factors and treatment responses focusing, as exploratory use cases, on neurodegenerative and gut microbiome related disorders. HEREDITARY is harmonizing and linking various sources of clinical, genomic, and environmental data on a large scale. This enables clinicians, researchers, and policymakers to understand these diseases better and develop more effective treatment strategies. HEREDITARY adheres to the citizen science paradigm to ensure that patients and the public have a primary role in guiding scientific and medical research while maintaining full control of their data. Our goal is to change the way we approach healthcare by unlocking insights that were previously impossible to obtain.